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Characterization and optimization of the non-viral gene
transfer vehicle Artificial viral particles (AVP)
Dissertation
zur Erlangung des akademischen Grades doctor rerum naturalium
(Dr. rer. nat.)
vorgelegt dem Rat der Biologisch-Pharmazeutischen Fakultät
der Friedrich-Schiller- Universität Jena
von Roman Egle
geboren am 03.08.1975 in München
















Gutachter:
1. Prof Dr. Udo Bakowsky, Philipps-Universität Marburg
2. Prof. Dr. Alfred Fahr, Friedrich-Schiller-Universität Jena
3. Prof. Julijana Kristl, PhD, University of Ljubljana, Slowenien
Öffentliche Disputation am 17. März 2008







Science may set limits to knowledge, but should not set limits
to imagination
Bertrand Russell (1872 1970)











For my parents

Acknowledgments
The completion of this thesis would not have been possible without many people s support.
First and foremost, I would like to thank my mentor Prof. Dr. Alfred Fahr for giving me the
possibility to do research in this exciting field and for supporting and guiding me throughout
the course of my Ph.D. project.
I would like to extend my gratitude to my friends, colleagues and former colleagues at
the department. They accompanied and helped me throughout the sometimes turbulent years.
I am grateful for Angela Herre s help in cell culture, Ina Lehmann s help with confocal laser
scanning microscopy, Steffi Richter s help in all fields of electron microscopy and for Dr.
Xiangli Liu s proofreading. I am especially grateful to Christian Rothkopf who guided my
first steps as freshman in the field of nanotechnology and cell culture.
I appreciate the co-operation with the team of Prof. Dr. Karl-Jürgen Halbhuber at the
Institut für Anatomie II in Jena. I am indebted to Dr. Oehring and Alida Braunschweig for the
preparation and examination of ultrathin sections of cells and to Frank Steiniger for Cryo-
TEM preparations.
I am also indebted to Prof. Dr. Michael Köhler, Jörg Wagner and Frances Möller from
the TU Ilmenau for providing me with a static micromixer, know-how and advice.
Furthermore, I would like to thank Dr. Lars Tönges from the University of Göttingen
for performing siRNA experiments together with me.
Spending one year of my research abroad constituted a highlight in my professional
and private life. For making this experience possible I am thankful to my host supervisors in
Slovenia: Prof. Dr. Julijana Kristl and Prof. Dr. Irena Mlinaric-Rascan and again to my home
supervisor Prof. Dr. Alfred Fahr. My warm thanks goes to the whole team in Ljubljana for
making me feel welcome. Especially to my office colleagues Andrej Dolenc and Matej Pavli
and to Miha Milek who introduced me into the mysteries of biochemistry without loosing
patience. This research year abroad has been supported by a Marie Curie Early Stage
Research Training Fellowship of the European Community s Sixth Framework Programme
under contract number MEST-CT-2004-504992.
I want to thank all my friends who encouraged and supported me. Special thanks go to
Dr. René Korn and to Franz Nagl for always being there to help or just to listen, for
motivating me when necessary and for proofreading.
Finally, I would like to express my deepest thanks to my family, especially to my parents.

Table of contents
Table of contents
1 Introduction
1.1 Gene therapy and used vectors 1
1.2 Artificial viral particles (AVP) 5
1.3 Physical characterization of gene carrier vehicles 7
1.4 Biological characterization of gene carrier vehicles 9
1.5 Tracing gene carrier particles in cells 12
1.6 Aim of the work 14
2 Materials and Methods
2.1 Methods
2.1.1 Preparation of artificial viral envelope AVE liposomes 15
2.1.2 DNA complexation agents (Polyethylenimine (PEI), Protamine sulfate,
Poly-l-Lysin and preparation of fluorescence marked PEI) 16
2.1.3 Preparation of Artificial viral particles (AVP) 17
2.1.4 Photon correlation spectroscopy 18
2.1.5 Zeta potential measurement 18
2.1.6 Transmission electron microscopy 19
2.1.7 Preparation of ultrathin sections of transfected cells for electron microscopy 20
2.1.8 Ultracentrifugation 20
2.1.9 E.coli transformation and plasmid amplification and purification 21
2.1.10 Agarose gel electroporesis 21
2.1.11 Marking plasmids with gold nanoparticles 22
2.1.12 Cell culture 23
2.1.13 Transfection procedure 23
2.1.14 Flow cytometry 24
2.1.15 Sulforhodamin B (SRB) toxicity assay 25
2.1.16 Confocal laser scanning microscopy 25
2.1.17 DNA quantitation with Picogreen ® and modifications to
decomplex DNA from PEI-DNA or AVP samples 26
2.2 Buffer and solvents 26

Table of contents
3 Results and Discussion
3.1 Characterization of AVP structure and structure activity relation 29
3.1.1 AVP characterization by Dynamic Light Scattering and Zetapotential 29
measurements
3.1.2 Structure of AVP in transmission electron microscopy 31
3.1.3 AVP separation by Ultracentrifugation 38
3.2 Tracking AVP into cells 43
3.2.1 Marking AVP with gold nanoparticles and tracing them by electron microscopy 43
3.2.2 Tracing fluorescence marked AVP into the cell 54
3.3 Continuous production of AVP in a static mixer 59
3.3.1 Early mixers 59
3.3.2 Use of the static chipmixer "Statmix 6" to produce AVP 64
3.3.3 Troubleshooting for AVP production in Statmix 6 71
3.4 AVP variations and impact on structure and biological
efficiency 79
3.4.1 Role of condensation agent 79
3.4.2 Variation of lipid composition 87
3.4.3 Dependence of AVP formation from shear forces 92
3.5 Employing AVP for novel cell culture applications 95
3.5.1 Competitiveness of AVP for siRNA transfection 95
3.5.2 Using AVP to explore the role of the enzyme
Thiopurine-S-methyltransferase (TPMT) in stable transfected cells 96
3.6 Observations and comments on testing AVP in vitro 100
4. Concluding summary and outlook: 104
Appendix: References, Abbreviations, Zusammenfassung, Curriculum Vitae, Publications
Introduction
1. Introduction
1.1 Gene therapy and used vectors
Gene therapy is one of the big issues in medicine and biotechnology. The vast theoretical
possibilities and the partially disillusioning experience in clinical trials raise hopes and fears
and form a controversial topic. The basic principle of gene therapy, treating diseases by
inserting or modifying genes also implicates the possibility to cure hereditary diseases such as
cystic fibrosis or muscular dystrophy.
After a promising start, the successful treatment of severe combined immunodeficiency of a
four year old girl in 1990 (Blaese et al., 1995), also unexpected dangers became apparent and
resulted in the death of an 18 year old man in a clinical trial that was intended to treat his
metabolic disease in 1999 (Teichler Zallen, 2000). This sad event resulted in a more cautious
and restricted handling of gene therapy trials (Smith, Byers, 2002; Thompson, 2000). Also
recent promising trials that improved hereditary immunodeficiency in three patients (Ott et
al., 2006) got a bitter aftertaste by the tragic death of one of the patients (Zinkant, 2006). Up
to now Gendicine , approved 2004 in China (Pearson et al., 2004; Peng, 2005), is the only
gene therapy drug that has been approved for commercial use worldwide and its approval is
also subject to critical discussion (Guo, Xin, 2006). In summary this promising field is still at
the beginning and further research is needed.
Gene therapy can be divided into the areas germline therapy and somatic therapy. In germline
therapy germ cells, ovum and sperm cells or their precursors, would be manipulated and the
changed genetic information would not only be incorporated into the manipulated cells, but
also inherited to future generations descending from those cells. This lasting engineering of
the germline is highly controversial and mainly rejected for human beings from an ethical
point of view (Rabino, 2003). Medical trials in humans are performed, at least up to now, only
in the field of somatic gene therapy. In somatic gene therapy target cells not involved in the
reproduction of the organism are genetically modified to heal an individual or improve its
condition. Somatic gene therapy can be subdivided into ex vivo therapy and in vivo therapy. In
ex vivo therapy target cells are taken from the body of the patient, genetically changed, and
reinserted. In in vivo gene therapy cells are modified in the body of the patient. This demands
specific targeting of the modification to its target cells.
1
Introduction
In vivo therapy:Ex vivo therapy:
The transfection vector is brought directly into the bodyCells are taken from the body,
to transfect target cells transfected ex vivo and reinserted
Fig 1.1 Ex vivo and in vivo somatic gene therapy
To bring genetic material successfully into cells, in other words to transfect them, either
physical methods or a transporter construct can be used. Examples for physical methods are
direct injection of naked DNA into muscle tissue (Davis et al., 1993) electroporation (Gehl,
2003), sonoporation and the gene gun where gold-nanoparticles coated with genetic
material are shot into cells (Mehier-Humbert, Guy, 2005).
Using a transporter construct, a so called vector, to ferry the genetic material into the cell,
seems a more elegant way. Nature developed very successful vectors: the viruses. They have
to bring their own genetic material into host cells in order to replicate. As they were optimized
by evolution over many millions of years they are extremely successful. Viruses that are
genetically modified to be unable to replicate and cause disease can be used to bring
therapeutic genetic material as payload into cells. This method is very efficient (Gardlik et al.,
2005) and is therefore used frequently. 67.4 % of the ongoing or completed clinical gene
therapy trials are using viral vectors (Adenovirus, Adeno-associated virus, Retrovirus,
Vaccinia virus, Poxvirus, Herpes simplex virus, ) according to an online overview (The
Journal of Gene Medicine, 2007). The above mentioned first approved gene therapy drug
Gendicine is also based on an adenovirus.
But the use of viral vectors derived from pathogens poses the possible danger of
recombination to a pathogen virus (Fischer, 2001) and even malignant disorders (Baum et al.,
2003). As the host organisms have developed counter mechanism against viral infections, also
unwanted immune reactions can be triggered (Lehrman, 1999).
2
Introduction
Therefore, there is intensive research to develop, characterize and optimize non-viral gene
transfer vectors as an alternative (Brown et al., 2001). As non-viral vectors are not derived
from pathogens they lack risks of viral vectors and promise to be safer (Nabel et al., 1993).
To result in good transfection, the successful introduction of foreign DNA into the cell, such a
vector has to overcome several obstacles (Wiethoff, Middaugh, 2003):
- The genetic material has to be compacted to be protected from degrading enzymes and
allow transportation.
- The vector needs to bring its payload across the cell membrane.
- The material has to be freed from endosomes, before being digested.
- DNA as payload has to be brought to the nucleus to be transcripted (copied into
mRNA).
For a possible in vivo use the vector also should:
- Be non-toxic
- Show low immunogeneticity
- Be stable in serum and blood
- Allow modifications to target it on specific organs or types of cells
And for routine use an easy, cost effective and reproducible manufacturing method is needed.
Genetic material such as DNA is charged negatively at physiological pH because of its
phosphate groups. Therefore, it can be sized down and protected by complexing it with a
cationic reagent. An early direct approach in this direction is the formation of co-precipitates
of DNA with Calcium phosphate (Chen, Okayama, 1987). Other reagents of the first
generation of gene transfer vehicles were pure cationic reagents like liposomes and polymers.
Liposomes containing cationic lipids such as DOTAP (1,2-dioleoyl-3-trimethylammonium-
propane), DOTMA (N-[1-(2,3,-dioleyloxy)propyl]-N,N,N-trimethylammonium), or DOSPA
(2,3-dioleyloxy-N-[2(sperminecarboxamido)-ethyl]-N,N-dimethyl-1-propanaminium trifluoro
acetate) form complexes with DNA, so called lipoplexes. Those lipoplexes were used to
transfect cells in cell culture (Behr, 1989; Torchilin, Weissig, 2003; Felgner et al., 1987), and
were especially effective when combined with helper lipids like DOPE (1,2-Dioleoyl-sn-
Glycero-3-Phosphoethanolamine) (Hirsch-Lerner et al., 2005). 7.6 % of the ongoing or
completed clinical gene therapy trials involved lipofection according to an online overview
(The Journal of Gene Medicine, 2007). This number is small compared to the number of virus
3

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